|
| Status |
Public on Sep 29, 2020 |
| Title |
blood_ctrl_P68 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood, patient 68, prior to treatment
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: relapse remitting multiple sclerosis (MS)
tissue: whole blood
treatment: none
time point: baseline
sample_pair: 68
sample type: control
|
| Treatment protocol |
Peripheral blood was drawn in PaxGene tubes (BD) at baseline and after 14 days of treatment. Blood tubes were gently inverted multiple times and allowed to rest for two hours to ensure RNA stability. Samples were frozen on -80°C for subsequent RNA purification.
|
| Growth protocol |
Relapse remitting MS patients were recruited at the St. Josef Hospital Bochum following inclusion and exclusion criteria of ethic approval from the Ruhr-University Bochum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of whole RNA was performed after manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA). In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.
|
| |
|
| Hybridization protocol |
3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640.
|
| Scan protocol |
Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.
|
| Description |
P190_03_68-1
|
| Data processing |
Data processing was performed using BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team.
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Sep 29, 2020 |
| Contact name |
Ori Staszewski |
| E-mail(s) |
ori.staszewski@uniklinik-freiburg.de
|
| Organization name |
University Medical Center Freiburg
|
| Department |
Institute of Neuropathology
|
| Street address |
Breisacher Str. 64
|
| City |
Freiburg |
| ZIP/Postal code |
D-79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE116835 |
Expression data from human whole blood of propionate treated MS patients |
|
